GapMind for catabolism of small carbon sources

 

L-arabinose catabolism in Azohydromonas australica DSM 1124

Best path

araE, xacB, xacC, xacD, xacE, xacF

Rules

Overview: L-arabinose utilization in GapMind is based on MetaCyc pathways L-arabinose degradation I, via xylulose 5-phosphate (link); III, oxidation to 2-oxoglutarate (link); and IV, via glycolaldehyde (link). Pathway II via xylitol and xylulose is not represented in GapMind because it is not reported in prokaryotes (link).

40 steps (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
araE L-arabinose:H+ symporter
xacB L-arabinose 1-dehydrogenase H537_RS0139985 H537_RS0110980
xacC L-arabinono-1,4-lactonase H537_RS0107150 H537_RS0107640
xacD L-arabinonate dehydratase H537_RS0137420 H537_RS0125690
xacE 2-dehydro-3-deoxy-L-arabinonate dehydratase H537_RS0137415 H537_RS0121535
xacF alpha-ketoglutarate semialdehyde dehydrogenase H537_RS0101950 H537_RS0121615
Alternative steps:
aldA (glycol)aldehyde dehydrogenase H537_RS0120085 H537_RS0138620
aldox-large (glycol)aldehyde oxidoreductase, large subunit
aldox-med (glycol)aldehyde oxidoreductase, medium subunit
aldox-small (glycol)aldehyde oxidoreductase, small subunit H537_RS43460 H537_RS0131420
araA L-arabinose isomerase
araB ribulokinase
araD L-ribulose-5-phosphate epimerase
araF L-arabinose ABC transporter, substrate-binding component AraF
araG L-arabinose ABC transporter, ATPase component AraG H537_RS42805 H537_RS41140
araH L-arabinose ABC transporter, permease component AraH
araS L-arabinose ABC transporter, substrate-binding component AraS
araT L-arabinose ABC transporter, permease component 1 (AraT)
araU L-arabinose ABC transporter, permease component 2 (AraU) H537_RS0139465
araUsh L-arabinose ABC transporter, substrate-binding component AraU(Sh)
araV L-arabinose ABC transporter, ATPase component AraV H537_RS0114820 H537_RS0104880
araVsh L-arabinose ABC transporter, ATPase component AraV(Sh) H537_RS0131585 H537_RS41140
araWsh L-arabinose ABC transporter, permease component 1 AraW(Sh)
araZsh L-arabinose ABC transporter, permease component 2 AraZ(Sh)
BT0355 L-arabinose:Na+ symporter
chvE L-arabinose ABC transporter, substrate-binding component ChvE
Echvi_1880 L-arabinose:Na+ symporter
gguA L-arabinose ABC transporter, ATPase component GguA H537_RS0131585 H537_RS42805
gguB L-arabinose ABC transporter, permease component GguB
glcB malate synthase H537_RS0135195
gyaR glyoxylate reductase H537_RS0111215 H537_RS0107560
KDG-aldolase 2-dehydro-3-deoxy-L-arabinonate aldolase
xacG L-arabinose ABC transporter, substrate-binding component XacG
xacH L-arabinose ABC transporter, permease component 1 (XacH) H537_RS0139460
xacI L-arabinose ABC transporter, permease component 2 (XacI) H537_RS0139465
xacJ L-arabinose ABC transporter, ATPase component 1 (XacJ) H537_RS48490 H537_RS0114820
xacK L-arabinose ABC transporter, ATPase component 2 (XacK) H537_RS48490 H537_RS0114820
xylFsa L-arabinose ABC transporter, substrate-binding component XylF
xylGsa L-arabinose ABC transporter, ATPase component XylG H537_RS0104880 H537_RS41140
xylHsa L-arabinose ABC transporter, permease component XylH

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory